An integrated tool for loop calculations: aITALC

aITALC, a new tool for automating loop calculations in high energy physics, is described. The package creates Fortran code for two-fermion scattering processes automatically, starting from the generation and analysis of the Feynman graphs. We describe the modules of the tool, the intercommunication between them and illustrate its use with three examples.

Program summary

Title of the program:aITALC version 1.2.1 (9 August 2005)Catalogue identifier:ADWOProgram summary URL:http://cpc.cs.qub.ac.uk/summaries/ADWOProgram obtainable from:CPC Program Library, Queen's University of Belfast, N. IrelandComputer:PC i386Operating system:GNU/Linux, tested on different distributions SuSE 8.2 to 9.3, Red Hat 7.2, Debian 3.0, Ubuntu 5.04. Also on SolarisProgramming language used:GNU Make, Diana, Form, Fortran77Additional programs/libraries used:Diana 2.35 (Qgraf 2.0), Form 3.1, LoopTools 2.1 (FF)Memory required to execute with typical data:Up to about 10 MBNo. of processors used:1No. of lines in distributed program, including test data, etc.:40 926No. of bytes in distributed program, including test data, etc.:371 424Distribution format:tar gzip fileHigh-speed storage required:from 1.5 to 30 MB, depending on modules present and unfolding of examplesNature of the physical problem:Calculation of differential cross sections for e⁺e⁻ annihilation in one-loop approximation.Method of solution:Generation and perturbative analysis of Feynman diagrams with later evaluation of matrix elements and form factors.Restriction of the complexity of the problem:The limit of application is, for the moment, the 2→2 particle reactions in the electro-weak standard model.Typical running time:Few minutes, being highly depending on the complexity of the process and the Fortran compiler.     

A framework for weighted fusion of multiple statistical models of shape and appearance

This paper presents a framework for weighted fusion of several active shape and active appearance models. The approach is based on the eigenspace fusion method proposed by Hall et al., which has been extended to fuse more than two weighted eigenspaces using unbiased mean and covariance matrix estimates. To evaluate the performance of fusion, a comparative assessment on segmentation precision as well as facial verification tests are performed using the AR, EQUINOX, and XM2VTS databases. Based on the results, it is concluded that the fusion is useful when the model needs to be updated online or when the original observations are absent     

An efficient model for studying the dynamics of frustrated systems

We present a model based on determinist cellular automata architecture for studying systems with frustrated interactions that present elemental excitations, such as magnetic monopoles. This model is especially designed to be applied for systems with components that have energy levels much higher than $kT$. This would imply that for these systems thermal fluctuations are negligible and they can be analyzed under the supposition that the dynamic is produced at zero temperature. This category includes artificial magnetic spin ice systems and donor and recipient electrical charge molecular systems. The dynamics of these systems can be simulated in real time with this model, with a minimum of computational requirements. It can be an excellent complement to Monte Carlo methods and in some cases can even replace them directly. In this report, we show the designed structure and some interesting results obtained in studying the dynamics of emergent magnetic monopoles in artificial spin ice systems and excitations in graphane molecular arrays.     

Stress recovery in geometrically nonlinear membranes by a Hu-Washizu finite element formulation

A class of mixed finite elements based on the Hu-Washizu functional is introduced as a strategy to reduce the spurious stress phenomena encountered with standard or displacement-based formulations for geometrically exact membranes. Selected examples compare the performance of this class of elements with that of the standard formulation and demonstrate that reduction of spurious stresses is obtained and that the stresses are more accurate than those optimally sampled in the standard formulation.     

Specific Local Predictors That Reflect the Tropism of Endometriosis—A Multiple Immunohistochemistry Technique

Ectopic endometrial epithelium associates a wide spectrum of symptomatology. Their evolution can be influenced by inflammatory and vascular changes, that affect not only the structure and cell proliferation rate, but also symptoms. This prospective study involved tissue samples from surgically treated patients, stained using classical histotechniques and immunohistochemistry. We assessed ectopic endometrial glands (CK7+, CK20−), adjacent blood vessels (CD34+), estrogen/progesterone hormone receptors (ER+, PR+), inflammatory cells (CD3+, CD20+, CD68+, Tryptase+), rate of inflammatory cells (Ki67+) and oncoproteins (BCL2+, PTEN+, p53+) involved in the development of endometriosis/adenomyosis. A CK7+/CK20− expression profile was present in the ectopic epithelium and differentiated it from digestive metastases. ER+/PR+ were present in all cases analyzed. We found an increased vascularity (CD34+) in the areas with abdominal endometriosis and CD3+−:T-lymphocytes, CD20+−:B-lymphocytes, CD68+:macrophages, and Tryptase+: mastocytes were abundant, especially in cases with adenomyosis as a marker of proinflammatory microenvironment. In addition, we found a significantly higher division index-(Ki67+) in the areas with adenomyosis, and inactivation of tumor suppressor genes-p53+ in areas with neoplastic changes. The inflammatory/vascular/hormonal mechanisms trigger endometriosis progression and neoplastic changes increasing local pain. Furthermore, they may represent future therapeutic targets. Simultaneous-multiple immunohistochemical labelling represents a valuable technique for rapidly detecting cellular features that facilitate comparative analysis of the studied predictors.     

Elevation of Tear MMP-9 Concentration as a Biomarker of Inflammation in Ocular Pathology by Antibody Microarray Immunodetection Assays

Matrix metalloproteinases are a family of enzymes fundamental in inflammatory processes. Between them, MMP-9 is up-regulated during inflammation; thus, its quantification in non-invasive fluids is a promising approach for inflammation identification. To this goal, a biomarker quantification test was developed for ocular inflammation detection using anti-MMP-9 antibody microarrays (AbMAs). After validation with eight healthy control tear samples characterized by ELISA, 20 samples were tested from individuals diagnosed with ocular inflammation due to: cataracts, glaucoma, meibomian gland dysfunction, allergy, or dry eye. Concentration values of tear MMP-9 were obtained for each sample, and 12 patients surpassed the pathological threshold (30 ng/mL). A significant elevation of MMP-9 concentration in the tears of glaucoma patients compared with healthy controls was observed. In order to evaluate the diagnostic ability, an ROC curve analysis was performed using our data, determining the optimal threshold for the test at 33.6 ng/mL of tear MMP-9. In addition, a confusion matrix was applied, estimating sensitivity at 60%, specificity at 88%, and accuracy at 68%. In conclusion, we demonstrated that the AbMAs system allows the quantification of MMP-9 in pathologies that involve inflammation of the ocular surface.     

Dipotassium Glycyrrhizinate on Melanoma Cell Line: Inhibition of Cerebral Metastases Formation by Targeting NF-kB Genes-Mediating MicroRNA-4443 and MicroRNA-3620—Dipotassium Glycyrrhizinate Effect on Melanoma

Glycyrrhizic acid (GA), a natural compound isolated from licorice (Glycyrrhiza glabra), has exhibited anti-inflammatory and anti-tumor effects in vitro. Dipotassium glycyrrhizinate (DPG), a dipotassium salt of GA, also has shown an anti-tumor effect on glioblastoma cell lines, U87MG and T98G. The study investigated the DPG effects in the melanoma cell line (SK-MEL-28). MTT assay demonstrated that the viability of the cells was significantly decreased in a time- and dose-dependent manner after DPG (IC₅₀ = 36 mM; 24 h). DNA fragmentation suggested that DPG (IC₅₀) induced cellular apoptosis, which was confirmed by a significant number of TUNEL-positive cells (p-value = 0.048) and by PARP-1 [0.55 vs. 1.02 arbitrary units (AUs), p-value = 0.001], BAX (1.91 vs. 1.05 AUs, p-value = 0.09), and BCL-2 (0.51 vs. 1.07 AUs, p-value = 0.0018) mRNA compared to control cells. The proliferation and wound-healing assays showed an anti-proliferative effect on DPG-IC₅₀-treated cells, also indicating an inhibitory effect on cell migration (p-values < 0.001). Moreover, it was observed that DPG promoted a 100% reduction in melanospheres formation (p-value = 0.008). Our previous microRNAs (miRs) global analysis has revealed that DPG might increase miR-4443 and miR-3620 expression levels. Thus, qPCR showed that after DPG treatment, SK-MEL-28 cells presented significantly high miR-4443 (1.77 vs. 1.04 AUs, p-value = 0.02) and miR-3620 (2.30 vs. 1.00 AUs, p-value = 0.01) expression compared to control cells, which are predicted to target the NF-kB, CD209 and TNC genes, respectively. Both genes are responsible for cell attachment and migration, and qPCR revealed significantly decreased CD209 (1.01 vs. 0.54 AUs, p-value = 0.018) and TNC (1.00 vs. 0.31 AUs, p-value = 2.38 × 10⁻⁶) mRNA expression levels after DPG compared to untreated cells. Furthermore, the migration of SK-MEL-28 cells stimulated by 12-O-tetradecanoylphorbol-13-acetate (TPA) was attenuated by adding DPG by wound-healing assay (48 h: p-value = 0.004; 72 h: p-value = 7.0 × 10⁻⁴). In addition, the MMP-9 expression level was inhibited by DPG in melanoma cells stimulated by TPA and compared to TPA-treated cells (3.56 vs. 0.99 AUs, p-value = 0.0016) after 24 h of treatment. Our results suggested that DPG has an apoptotic, anti-proliferative, and anti-migratory effect on SK-MEL-28 cells. DPG was also able to inhibit cancer stem-like cells that may cause cerebral tumor formation.     

Spanish Melon Landraces: Revealing Useful Diversity by Genomic,Morphological, and Metabolomic Analysis

Spain is a secondary centre of the diversification of the melon (Cucumis melo L.), with high diversity represented in highly appreciated landraces belonging to the Flexuosus and Ibericus groups. A collection of 47 accessions of Flexuosus, Chate, Piel de Sapo, Tendral, Amarillo, Blanco, and Rochet was analysed using a genotyping-by-sequencing (GBS) approach. A total of 66,971 quality SNPs were identified. Genetic analysis differentiated Ibericus accessions and exotic materials (Ameri, Momordica, Kachri, and Agrestis), while Flexuous accessions shared ancestry between them. Within the Ibericus group, no clear genomic distinction could be identified for the different landraces evaluated, with accessions of different landraces showing high genetic similarity. The morphological characterization confirmed that the external colour and fruit shape had been used as recognition patterns for Spanish melon landraces, but variability within a landrace exists. Differences were found in the sugars and acid and volatile profiles of the materials. Flexuosus and Chate melons at the immature commercial stage accumulated malic acid and low levels of hexoses, while Ibericus melons accumulated high contents of sucrose and citric acid. Specific trends could be identified in the Ibericus landraces. Tendral accumulated low levels of sugars and citric acid and high of malic acid, maintaining higher firmness, Rochet reached higher levels of sugars, and Amarillo tended to lower malic acid contents. Interestingly, high variability was found within landraces for the acidic profile, offering possibilities to alter taste tinges. The main volatile organic compounds (VOCs) in Flexuosus and Chate were aldehydes and alcohols, with clear differences between both groups. In the Ibericus landraces, general trends for VOC accumulation could be identified, but, again, a high level of variation exists. This situation highlights the necessity to develop depuration programs to promote on-farm in situ conservation and, at the same time, offers opportunities to establish new breeding program targets and to take advantage of these sources of variation.